The Miracle
by MarillaT'Pel
Summary: Some events after the movie, with certain details changed, and a very important conversation between Sam and Tron.  I don't own anything.


**In this story, Flynn never actually told Sam what the miracle was. This is how it would have happened if someone as sappy as me had written it. Oh, and Tron is in the real world with them. Pairings include bits of Tron/Sam friendship and hero worship (which may seem a little slashy, I admit, so there's your warning) and Jet/Quorra. This story includes Jet, a character (as far as I know) present only in games, and some events from the graphic novel Tron: Betrayal. I haven't actually read it, so I hope it sounds right!**

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><p>The Miracle<p>

_It was getting late. A busy father was telling his son a bedtime story before he left for work._

"_The Grid. A digital frontier. I tried to picture clusters of information as they moved through the computer. What did they look like? Ships, motorcycles? Were the circuits like freeways? I kept dreaming of a world I thought I'd never see. And then, one day..."_

"_You got in!"_

"_Heh heh. That's right, man... I got in! And the world was more beautiful than I ever dreamed, and also, more dangerous than I ever imagined. Hop into bed now." As seven year old Sam Flynn did as his father, Kevin, said he continued with the story. "Now, I met a brave warrior…"_

"_Tron!" Interrupted Sam, excitedly. Kevin handed him a figure._

"_Tron."_

"_He fights for the users." Added Sam._

"_He sure does." Said Kevin. "Oh man, he showed me things that no one had ever imagined, disk battles fought in spectacular arenas, cycles that raced on ribbons of light, so radical. And together…" he trailed off, waiting for his son to speak up._

"_You built the Grid."_

"_We built a new Grid, for programs and users. Now, I couldn't be in there all the time, so I created a program, in my own image, that could think like you and me. And I called him C.L.U." He handed Sam a second figure._

"_Codified Likeness Utility."_

"_That's right. And Clu, Tron, and I built a system where all information was free and open, beautiful." He paused, and his eyes moved to gaze somewhere over Sam's shoulder. "And then one day, something happened. Something extraordinary. A miracle." His eyes seemed to lose focus, almost as if he was trying to look through the wall and into the past._

"_What was it?" Asked Sam. He'd never heard this part of the story before. Kevin smiled at him._

"_That'll have to wait till next time. I've gotta get to work."_

"_I wanna go with you, Dad." Said Sam._

"_Yeah, well, one day you will. I promise."_

"_To the Grid?" Asked Sam, eagerly. His father smiled._

"_Good night, Sam." He stood up and pulled on his jacket. "Hey, what do you say tomorrow, you and I hit the arcade? You can have a crack at the old man's high score. First game's on me." He flipped a quarter toward his son, who caught it, and headed for the bedroom door._

"_Can we play doubles? On the same team?" His father turned back to him and smiled warmly._

"_We're always on the same team." He shut off the light and disappeared from his son's life for the next twenty years._

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><p>It was all finished. Sam sat before the computer in his new apartment where he'd been putting the finishing touches on his modifications. He'd moved to be closer to ENCOM after choosing to invoke his right to be involved in its goings on. It was also because he now had two programs living with him. He thought back on the past three weeks.<p>

He and Quorra had been right there, about to go through the portal, when he had seen his father fighting Clu. Sam had tried to run back, but Quorra had held on to him. Then, out of nowhere, Rinzler, no Tron, had emerged. His circuitry had changed from orange back to white, like theirs. He started over to the battling user and program, only to stop when Flynn shouted something at him. He then turned and began running toward the portal instead. Sam, who'd managed to shake Quorra off, was trying to get back to help his father. Before he could get far, though, Tron intercepted him and dragged him right back to the portal.

Looking over the program's shoulder at his father holding Clu off, Sam knew that it was his wish for them to all escape back to the real world. He resigned himself to that fact and lifted the disc high above his head, feeling himself being pulled home, with two guests in tow. The last thing he saw before he left was his father disappearing with Clu.

They'd arrived in the basement of the old arcade, the morning after he'd arrived there. Sam didn't bother to question how he'd gotten his old clothes back, or how the two computer programs were able to become flesh and blood, looking relatively unchanged except for the lack of circuitry. He would worry about it later. First, he just wanted to create a backup file of the system. His two guests both seemed to be in shock. He could understand why; they'd both lost someone dear to them and found themselves in a whole new world.

Alan had arrived not long after they got back. Sam was grateful for that, as he didn't have enough room on his bike to get both Tron and Quorra back to his place, and he wasn't sure it was a good idea to ferry them separately. He'd looked at them, more than a little confused.

"Sam," he said, not taking his eyes off of them, "who are your friends?" Sam gestured at Quorra to his right.

"This is Quorra." He wasn't sure yet what she was to him. She'd lived with his father for years, looking to him for protection and guidance. He figured she'd probably looked to him as a father figure as well. He had no idea how to introduce Tron. So he looked at him and said, "I'm pretty sure you two know each other already."

As he spoke, Tron removed the helmet that had covered his face for years. Sam was shocked by how much he looked like Alan. Or rather, how much he looked like Alan in his early thirties. He'd been a little amused as he watched the program and user meeting face to face for the first time ever. Alan had been in awe of the fact that he was now looking at his creation brought to life. Tron had been equally in awe over literally meeting his maker.

For a moment, watching the two, Sam for forgot about the fact that his father was really gone and thought about how excited Jet, Alan's son, would be to meet Tron. Jet was just one year older than him and had often slept over at his house, listening to his father's stories about the Grid. Jet was the closest Sam had ever come to having a brother, especially after Alan had become his legal guardian, but they'd kind of lost touch when they got older. Jet's mother, Lora, had died when he was twelve and Sam was eleven. For Sam, whose own mother died when he only two years old, it was just as bad as losing a real mother. It had caused some serious trouble in his relationship with his father. He had immediately left home when he turned eighteen, Sam following his example a year later, unable to deal with Alan's suggestions of taking a role in the company's proceedings.

He shook himself out of his reminiscing. He and Alan needed to get the two programs back to his place in order to get them situated. They would need to be comfortable here; there was no telling how long it would be before they returned to the Grid or what state it would be in. His place was in no way suited for more than one person.

After getting them in the car and calling a truck for his bike (Tron and Quorra both refused to get in without him) they went back to Alan's apartment. Alan still had some of Jet's clothing, and it fit Tron well enough. They had to guess Quorra's size in order to get her something to wear. He might've found it funny to see Alan trying to figure out what Quorra would want to wear, but he'd had to stay with the two programs in order to make sure they didn't get into trouble.

Sleeping arrangements had posed another problem. Alan had a guest bedroom and a nice couch. Sam figured he'd just return home for the night, but once again, Tron and Quorra refused to let him go anywhere without them. They set Quorra up in the guestroom. Alan came close to suggesting that he give up his own room for Sam and Tron to share, but Sam wouldn't hear it. Alan was pushing sixty and he had a special mattress for a reason. Tron had insisted on giving Sam the couch. Sam had finally suggested flipping a coin, and won the couch fair and square, to Tron's satisfaction.

As he lay there that night, he finally allowed himself to process everything that had happened. His father was really gone. For years, he'd lived knowing that his father was probably dead. Even then, there'd always been some stubborn hope that he was alive that just wouldn't go away, even as he professed to have no hope of seeing him again. Now, after finding out that his father had been alive all these years, he'd lost him again.

The next day, Sam had begun looking for a new home that would suit his new guests, since they didn't seem at all inclined to stay anywhere else but with him. He'd found a nice place right away. Three bedrooms, two bathrooms, roomy, with an incredible view of the city below, and they even allowed pets. It wasn't all that different from his father's place on the Grid, except everything wasn't all white and glowing.

His first big priority, once getting them to their User world home, was teaching Tron and Quorra how to interact with other people. Obviously they couldn't just tell anyone who they really were. Only two other people knew about them, Alan and Jet Bradley. Sam had been right about how excited Jet was to meet them. He was in awe of their childhood hero, as well as the ISO. Though, he mused, Quorra had captured a little more than just his scientific interest. Sam certainly didn't blame him; she was very beautiful. She certainly didn't seem to mind the attention. Sam had felt an attraction for her at first, but the fact that his father had played such a paternal role in her life made him think of her as an almost sisterly presence in his.

Creating identities for them both had been a little difficult as well. Using their superior computer skills, Sam and the Bradley's had created birth certificates and other necessary paperwork for them. Officially, Quorra was Quorra Flynn, Sam's adopted sister who'd never been made official because of Kevin Flynn's disappearance, and Tron was Tron Bradley, Alan and Jet's oddly named cousin from Canada. It was all believable enough that no one would question the stories or look too closely at anything on their forged documents.

Sam thought back on some of what had happened in the three weeks that he'd been guardian to two homeless programs. Quorra had been delighted to learn how Users used computers. She'd also been excited to learn how to shop online. One of the first places Sam had taken her was a library, and she'd nearly had a fit over how many books she saw. However, returning them on time proved to be a problem, so Sam taught her how to order ones she could keep online.

It was fine, until he got the bill. In addition to books, she began ordering furniture and artwork that reminded her of the home she'd shared with Kevin. Between his considerable inheritance and his salary, Sam could definitely afford it, but he was accustomed to a simpler lifestyle, and she'd spent more on stuff in a week than he did in a month or two. And, he had to admit, seeing things that reminded him of that place heightened certain feelings of jealousy that he felt for Quorra. He knew there was no reason to feel animosity toward her over how everything had turned out, but it didn't completely stop the feelings of loss and regret over the fact that she'd had more time with his father than he had, or ever would. Though, he could usually banish those negative feelings by remembering the way Tron nearly jumped out of his new skin when he stepped on some bubble wrap that had come with said purchases and was scared by the gunshot-like popping sounds.

Explaining User life to the programs had been an adventure in itself. He had to 'translate' parts of daily living into terms they could understand. Eating and drinking was like refueling. Bathing to get rid of dirt and germs was like cleansing a system of potentially harmful bugs. Using the toilet was like trashing unnecessary leftover data. A driver's license was like an identity disk, though you couldn't fight with it. Quorra seemed to adapt to a lot of things faster than Tron, having lived with Flynn all those years. He'd taught her more about the User world, whereas with Tron, he'd spent more time working than teaching.

Sometimes, it was incredibly frustrating. The programs were very curious about the new world around them. Sometimes, it felt like having children. Two very large children who wanted to learn about every single thing that they saw (and often broke it in the process) as they explored new surroundings for the first time.

It was also hard housing two people who were so used to being warriors all the time. The first morning in their new place, Tron and Quorra had both rushed to defend him from a loud object threatening him in his bedroom. By the time he explained what an alarm clock was, it was too late to save it. Still, it was nice in some ways. Everything, even things he considered part of daily living that he didn't give thought to anymore, was something new and exciting to them. They both had an air childlike wonder about them.

One thing that helped was that Jet was more than willing to help him babysit. Both of them and Alan were all insanely busy with running ENCOM together. But in spite of how difficult it all could be, Sam couldn't help but notice how nice it felt to come home to someone. You know, other than a pet.

A glance at the clock told him he was running late. He'd been preparing almost non-stop for the past three weeks for a return to the Grid. Around his neck was the new and improved version of it all. It was just a start though. There would be plenty of improvements to be made once it was up and running. He knew Tron, Quorra, and Jet were all waiting for him at the arcade and it was getting dark. He pulled on his jacket, switched off the lights, and headed to his bike.

He arrived to find Jet standing outside, looking up and down the street for him.

"What the hell took you so long?" he snapped irritably.

"Sorry," said Sam, getting off the bike locking it up, "I had some last minute stuff I wanted to do." He grinned knowingly. "They tell you come out and look for me?"

"You know it." Muttered Jet. Despite their growing independence, Tron and Quorra were both still very attached to Sam, always wanting to know where he was and if he was safe. It made it a little difficult for Alan and Jet to look after them sometimes. As they descended the steps to the basement, Sam was met with the familiar worried faces of the two programs.

"Why are you late?" Asked Tron.

"We thought you were attacked or had an accident." Added Quorra.

"Nothing like that happened," assured Sam with a smile, "I just got caught up making a few last minute adjustments." He'd almost had them convinced he was perfectly safe without them around all the time. Then they'd started watching the news. After that they were both convinced that he could die any moment, whether it was from a car accident or a terrorist attack. He supposed he couldn't blame them. If he'd lost a dear friend, he'd probably want to make sure the people most important to that friend were alright afterward. He looked around at them. "Everybody ready to go?" They all nodded. Tron and Quorra were both eager to return and assist in the rebuilding of their home. It was unknown yet how they would divide their time between here and there, if they wanted to return to the user world at all. Quorra would, he was almost certain. She'd been dreaming about really seeing the user world for years, and now that she had, it was highly unlikely that just a few weeks would be enough to satisfy twenty years worth of curiosity. Tron was another story. While he'd been curious about User life, he'd been content enough with Flynn's stories. His main focus was always his job.

Sam plugged in the flash drive and began putting in the codes necessary to start rebooting the Grid. It would give them a basic outline to work with, and then they would fill in the blanks. Their plan was to make it even better than before. That done, he gathered them all in front of the digitizer. He'd had to tweak it a bit to make sure it would be able to take them all at once, a task he'd been nervous about since it was something that he'd only heard described in his father's bedtime stories prior to his adventure. He put in the code to activate it and felt the familiar unsettling feeling of being downloaded into the digital world.

Once they arrived, Sam handed out what they all needed. The plan was to leave special pieces of data around like seeds that would grow until they connected with the other's, reforming the landscape of the grid and bringing the programs back. Sam suggested they split into teams and go their separate ways until it was time to return in three hours. Jet immediately volunteered to pair up with Quorra, and they headed south while Sam and Tron went north.

As they moved around, planting their digital seeds, they made a little small talk. Sam decided now was as good a time as any to ask Tron about his plans for the future, and whether or not he planned to continue living in the real world or the new and improved Grid.

"Tron." The program immediately looked at him, letting him know he had his attention. "What are you planning on doing once the Grid is up and running again? Are you going to want to stay here, or come back to the User world, or what?" Tron cocked his head to one side.

"Flynn once told me that if anything ever happened to him, and I was in a position to do so, he wanted me to do whatever I could to protect his miracle." He smiled a little. "I'll go or stay wherever I have to in order to do that." Sam nodded.

"Okay, we'll ask Quorra what she wants to do and-" Tron cut him off there, looking confused.

"I'm not talking about Quorra." Now Sam was confused.

"What? You said you have to protect the miracle. She's the last of the ISO's." Tron studied him.

"Didn't Flynn tell you what the miracle was?" Tron knew the story of Sam's last night with his dad. He'd told him and Quorra both about it. Tron had seemed to light up a bit at the mention of the miracle, which had surprised Sam somewhat since he'd expected any reaction to that part of the story to come from Quorra. He also remembered when his father had first told him of the discovery of the ISO's. _The miracle_, he'd thought, but he'd remained silent. As he replayed that moment in his mind, he realized that his father had never actually _said_ that the ISO's were the miracle.

"No," he said, in answer to Tron's question, "I guess he never actually did." Tron almost looked a little sad now. He pulled his disk from his back and set it on the ground, pressing certain options that appeared before him.

"There's something you need to see." He said quietly, stepping back as images began to appear in the air before them, projected from his disk.

To Sam's amazement, he saw his father, looking even younger than he had when he disappeared, appear in the projection. With him were Tron and Clu. They appeared to be working on something to improve the Grid, when Flynn got a page, _in the Grid_, and hastily excused himself. As Clu remarked to Tron about how he thought it wasn't possible for there to be that kind of communication from the User world, Sam turned to the real Tron standing next to him.

"I don't get it." He said. "What's so important about this?" The images halted and Tron turned to answer him.

"That page was a message from your mother. Flynn gave her a special number so she could contact him, even while he was working in the Grid, with any details about you. She called him that day because you were about to be born." Before Sam could question him further, he turned back to the projection and it started up again. He watched as his father returned an unknown amount of time later and met Tron.

"_Flynn." He called out as he approached. "You were gone for quite some time. Is everything all right?" Kevin smiled broadly and grabbed Tron by the shoulders._

"_Jordan went into labor! It's a boy! We have a son! We're naming him Sam!" He shook Tron's shoulders joyfully._

"_That's wonderful Flynn." Replied Tron with a smile. "Are you ready to get back to work?" Flynn shook his head._

"_I can't stay. I have to get back to the hospital. We're brining Sam home today." Tron frowned._

"_But you will return at some point, won't you?"_

"_Sure." Replied Flynn. "But I have other things to think about now. Jordan and I have a baby, someone who's completely dependent on us and…it's just…" He trailed off for a moment. "I don't know how to describe it man. I never used to believe in miracles, that's why I work in furthering technology. I always believed in human ingenuity. But I believe now. I believe in miracles, because I see one every time I look at my little boy. Every time he opens his eyes or just takes another breath, I see one. That's what he is. He's my miracle." He blinked the tears out of his eyes. "I'll still come here to help you do whatever needs to be done, but I've got a whole family to think about now. And besides," he added with a smile, "that's why we have Clu. He's here to take care of business while I'm not around. He picked up the slack for me when I got married, and he'll do that again now." His smile broadened again. "God, it's been three days and I still almost can't believe I'm a father!" Tron just smiled, swept up in his friend's happiness._

The projection disappeared. Sam just stared at the space where it had been, not quite trusting himself to speak at first. It was Tron who broke the silence, once he'd reattached his disk.

"He stayed away for long periods of time after that. Clu was jealous, not just of the way Flynn was able to come and go, but of the fact that he cared more about you, your mother, and his life in the User world than him and the Grid, and the power he wielded over it. He thought that Flynn was undeserving of that power because of the fact that he was not completely devoted to his own cause. I think it lessened after your mother died, because he started spending a lot more time here, throwing himself into his work to try to forget. But then he started talking about how he wasn't being a good father hiding here all the time and that needed to spend more time taking care of you, and he started spending more time away. I think that, along with the fact that he viewed the ISO's as a serious flaw that had to be dealt with gave him the incentive to begin gathering support and strength to stage his coup." He paused. "I believe you know the rest." Sam just stared at him for a moment.

"It was me." He finally managed. Tron nodded.

"Yes Sam. The miracle was you." Sam just nodded.

"Thank you. For telling me that." Tron just nodded. Then he put his hand on Sam's shoulder and gave him a friendly little shake.

"Come on." He said. "We need to get this finished and head back." They finished planting their digital seeds, Sam almost moving in a daze, and made their way back to the portal. Jet and Quorra were already there. She was laughing at what was very likely a line he'd fed her, probably giving it more of a reaction than it deserved. They both looked up.

"Are you okay?" Asked Jet, looking a little concerned. Sam realized that some of what he was feeling must be showing on his face. He smiled at them.

"I'm good." He said. And he was. "Come on, let's go home." They all got into the portal and Sam triggered the ride home, knowing that he was going back with a sense of peace that he'd been lacking before. Maybe later, once he'd had time to properly sort out his feelings on what he'd just learned, he'd share it with the others. For now though, he was going home with his odd family and revel in this newfound happiness.

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><p><strong>The part at the beginning was copied with help from online movie quotes and clips, though it may not all be correct. Stuff about Jordan and Sam's birth comes from the aforementioned graphic novel. <strong>

**Obviously, this changes the scene where Sam finds out about the ISO's. Like I said, this is how it would have gone if I had written the movie script, which I did not. And as I said before, I'm a sap.**

**Thanks for reading and please review!**


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